density mod., NSC and software..

From: Tommi Kajander
Date: 20 December 2011 16:18

Dear all, 

Stupid question: if i do density modification (flattening and extension say from 6 to  4Å)

w/o averaging on a symmetrical, say dimer, would you expect the thing stays symmetric nevertheless?

(in particular if there is a strong peak in the NCS??) (seems to me it doenst necessarily...)

favorite programs for NCS averiging?? DM obviously, and solomon doesnt do it.  Others that do it

(with out a PDB or atoms to derive it from, but rather operators)

Thanks,

Tommi

Tommi Kajander, Ph.D., Docent

Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki

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From: Debreczeni, Judit

DM is kind of past tense (unless you are dealing with multicrystal averaging) -- I'd use parrot or shelxe instead (both pretty fast and automated). NCS operators as input do not seem to be in fashion these days, so you might have to put up with heavy atoms or partial MR models…

 

I would not necessarily expect NCS related bits of the density to be fully identical.

 

JED.

 

 

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From: Tommi Kajander

Thanks judit, well one problem here would be that if you cant feed in operators, that you got say from the map correlations with

something like GETAX, and you only have two sites (one per monomer) thats not enough to define a two-fold... same goes

of course if you dont have a model (because you would need to get the averaging to work first... )